Rhizomelic chondrodysplasia punctata

disease
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Also known as RCDPrhizomelic chondrodysplasia punctata syndromerhizomelic dwarfism

Summary

Rhizomelic chondrodysplasia punctata (MONDO:0015776) is a disease with 4 cohort genes and 2 clinical trials. The dominant Reactome pathway is Peroxisomal protein import (4 cohort genes). Top therapeutic interventions include ppi-1011.

At a glance

  • Prevalence: Unknown (Worldwide) [Orphanet-validated]
  • Cohort genes: 4
  • ClinVar variants: 130
  • Phenotypes (HPO): 20
  • Clinical trials: 2

Clinical features

Epidemiology

Prevalence records

2 prevalence record(s), Orphanet:

TypeClassValueGeographyValidation
Prevalence at birth1-9 / 1 000 0000.7EuropeValidated
Prevalence at birth1-9 / 1 000 0000.5United StatesValidated

Signs & symptoms

Clinical features (HPO)

20 HPO clinical features (Orphanet curated; top 20 by frequency):

HPO IDTermFrequency
HP:0000164Abnormality of the dentitionVery frequent (80-99%)
HP:0000252MicrocephalyVery frequent (80-99%)
HP:0000286EpicanthusVery frequent (80-99%)
HP:0000518CataractVery frequent (80-99%)
HP:0000944Abnormal metaphysis morphologyVery frequent (80-99%)
HP:0000958Dry skinVery frequent (80-99%)
HP:0001510Growth delayVery frequent (80-99%)
HP:0002231Sparse body hairVery frequent (80-99%)
HP:0002650ScoliosisVery frequent (80-99%)
HP:0004322Short statureVery frequent (80-99%)
HP:0005930Abnormality of epiphysis morphologyVery frequent (80-99%)
HP:0008064IchthyosisVery frequent (80-99%)
HP:0008905RhizomeliaVery frequent (80-99%)
HP:0009826Limb undergrowthVery frequent (80-99%)
HP:0010655Epiphyseal stipplingVery frequent (80-99%)
HP:0001376Limitation of joint mobilityFrequent (30-79%)
HP:0003298Spina bifida occultaFrequent (30-79%)
HP:0012368Flat faceFrequent (30-79%)
HP:0001596AlopeciaOccasional (5-29%)
HP:0010864Intellectual disability, severeOccasional (5-29%)

Identifiers

Disease identifiers

FieldValue
Canonical namerhizomelic chondrodysplasia punctata
Mondo IDMONDO:0015776
MeSHD018902
OMIM215100
Orphanet177
DOIDDOID:2580
ICD-10-CME71.540
ICD-11260357080
NCITC85047
SNOMED CT56692003
UMLSC0282529
MedGen79471
GARD0013160
Is cancer (heuristic)no

Also known as: RCDP · rhizomelic chondrodysplasia punctata · rhizomelic chondrodysplasia punctata syndrome · rhizomelic dwarfism

Data availability: 130 ClinVar variants · 12 cell lines.

Disease family

An umbrella term covering 4 Mondo subtypes.

Classification path: disease › human disease › disease by body system or component › disorder of orbital regioneye disorderrhizomelic chondrodysplasia punctata

Related subtypes (119): ptosis, eye accommodation disease, corneal disorder, asthenopia, lens disorder, keratomalacia, scleral disorder, ocular siderosis, coloboma, luxation of globe, mucopolysaccharidosis type 1, lacrimal apparatus disorder, Foster-Kennedy syndrome, anterior dislocation of lens, uveal disorder, eyelid disorder, ocular hypotension, scotoma, exophthalmos, ophthalmia nodosa, eye degenerative disorder, refractive error, glaucoma, retinal disorder, eye allergy, ocular vascular disorder, optic neuritis, conjunctival disorder, ocular hypertension, Tietz syndrome, Alagille syndrome, glaucoma-sleep apnea syndrome, Marshall syndrome, microcornea-glaucoma-absent frontal sinuses syndrome, nail-patella syndrome, oculodentodigital dysplasia, piebaldism, Sturge-Weber syndrome, cerebrotendinous xanthomatosis, ocular cystinosis, alpha-mannosidosis, megalocornea-intellectual disability syndrome, mucolipidosis type IV, mucopolysaccharidosis type 6, Netherton syndrome, galactosialidosis, Niemann-Pick disease type A, ocular motor apraxia, Cogan type, Peters plus syndrome, isolated Pierre-Robin syndrome, ectodermal dysplasia-blindness syndrome, Sandhoff disease, SHORT syndrome, Sjogren-Larsson syndrome, Smith-Lemli-Opitz syndrome, Tay-Sachs disease, tyrosinemia type II, Ito hypomelanosis, X-linked cone dysfunction syndrome with myopia, red color blindness, oculocerebrorenal syndrome, Lowry-MacLean syndrome, pigment dispersion syndrome, hereditary hyperferritinemia with congenital cataracts, dyssegmental dysplasia-glaucoma syndrome, mevalonic aciduria, familial cavitary optic disk anomaly, blindness - scoliosis - arachnodactyly syndrome, fatty acyl-CoA reductase 1 deficiency, microcephaly-intellectual disability-sensorineural hearing loss-epilepsy-abnormal muscle tone syndrome, neurotrophic keratopathy, Cogan syndrome, atopic keratoconjunctivitis, Ehlers-Danlos syndrome, kyphoscoliotic type 1, IRVAN syndrome, Rothmund-Thomson syndrome type 2, microcornea-corectopia-macular hypoplasia syndrome, isolated anophthalmia-microphthalmia syndrome, Spasmus nutans, toxic maculopathy due to antimalarial drugs, syndromic recessive X-linked ichthyosis, acute zonal occult outer retinopathy, acute annular outer retinopathy, phakomatosis pigmentovascularis, lamellar ichthyosis, idiopathic linear interstitial keratitis, chondroectodermal dysplasia with night blindness, galactosemia, GM1 gangliosidosis, Gaucher disease, visual snow syndrome, extensive peripapillary myelinated nerve fibers, IgG4-related ophthalmic disorder, global developmental delay-visual anomalies-progressive cerebellar atrophy-truncal hypotonia syndrome, vernal keratoconjunctivitis, Gardner syndrome, anterior segment dysgenesis, isolated ankyloblepharon filiforme adnatum, hereditary optic neuropathy, essential strabismus, Axenfeld anomaly, eye neoplasm, isolated blepharochalasis, punctate inner choroidopathy, eye infectious disorder, vitreous body disorder, 9q33.3q34.11 microdeletion syndrome, autoimmune/inflammatory optic neuropathy, LTBP2-related ocular dysgenesis, ocular growth disorder, ocular dysgenesis caused by defects in PAX6 regulation, choroidal neovascularization, anterior segment developmental abnormality with extraocular manifestations, congenital optic disk excavation, neuroocular syndrome, isolated angioid streaks, multiple evanescent white dot syndrome, stellate multiform amelanotic choroidopathy, macular telangiectasia

Subtypes (4): rhizomelic chondrodysplasia punctata type 1, rhizomelic chondrodysplasia punctata type 2, rhizomelic chondrodysplasia punctata type 3, peroxisome biogenesis disorder due to PEX5 defect in the PEX7-binding domain

Genetics & variants

GWAS landscape

No GWAS associations recorded — common-variant (GWAS) studies don’t cover this disease (typical for Mendelian / rare diseases). See the curated gene cohort and Mendelian overlap below.

Variant details and genetic-evidence tiers

ClinVar germline variants

130 retrieved; paginated sample, class counts are floors:

49 uncertain significance, 17 pathogenic/likely pathogenic, 17 likely benign, 17 likely pathogenic, 13 pathogenic, 7 benign, 6 conflicting classifications of pathogenicity, 4 benign/likely benign

ClinVarVariant (HGVS)GeneClassificationReview
3366567NC_000002.11:g.(178362494_178364345)_(178372760_178378546)delAGPSPathogeniccriteria provided, single submitter
1073464NM_014236.4(GNPAT):c.1583_1586del (p.Leu528fs)GNPATPathogeniccriteria provided, multiple submitters, no conflicts
190410NM_001351132.2(PEX5):c.677dup (p.Val227fs)PEX5Pathogeniccriteria provided, single submitter
1075998NM_000288.4(PEX7):c.474_477del (p.Tyr159fs)PEX7Pathogenic/Likely pathogeniccriteria provided, multiple submitters, no conflicts
1339708NM_000288.4(PEX7):c.376C>T (p.Gln126Ter)PEX7Pathogenic/Likely pathogeniccriteria provided, multiple submitters, no conflicts
1421713NM_000288.4(PEX7):c.517del (p.Ser173fs)PEX7Pathogenic/Likely pathogeniccriteria provided, multiple submitters, no conflicts
1449189NM_000288.4(PEX7):c.488G>A (p.Trp163Ter)PEX7Pathogenic/Likely pathogeniccriteria provided, multiple submitters, no conflicts
1486959NM_000288.4(PEX7):c.804-2A>CPEX7Pathogenic/Likely pathogeniccriteria provided, multiple submitters, no conflicts
188711NM_000288.4(PEX7):c.400G>A (p.Asp134Asn)PEX7Pathogenic/Likely pathogeniccriteria provided, multiple submitters, no conflicts
188975NM_000288.4(PEX7):c.188+1G>CPEX7Pathogenic/Likely pathogeniccriteria provided, multiple submitters, no conflicts
189076NM_000288.4(PEX7):c.618G>A (p.Trp206Ter)PEX7Pathogenic/Likely pathogeniccriteria provided, multiple submitters, no conflicts
1926974NM_000288.4(PEX7):c.858_867del (p.Glu287fs)PEX7Pathogenic/Likely pathogeniccriteria provided, multiple submitters, no conflicts
225436NM_000288.4(PEX7):c.183del (p.Phe61fs)PEX7Pathogenic/Likely pathogeniccriteria provided, multiple submitters, no conflicts
3619127NM_000288.4(PEX7):c.678G>A (p.Trp226Ter)PEX7Pathogenic/Likely pathogeniccriteria provided, multiple submitters, no conflicts
370629NM_000288.4(PEX7):c.13_19dup (p.Gly7fs)PEX7Pathogeniccriteria provided, multiple submitters, no conflicts
370682NM_000288.4(PEX7):c.277C>T (p.Gln93Ter)PEX7Pathogenic/Likely pathogeniccriteria provided, multiple submitters, no conflicts
4059703NM_000288.4(PEX7):c.903+2T>GPEX7Pathogeniccriteria provided, single submitter
4818131NM_000288.4(PEX7):c.804-2A>GPEX7Pathogeniccriteria provided, single submitter
4818134NM_000288.4(PEX7):c.901_903+3delinsAGPEX7Pathogeniccriteria provided, single submitter
554785NM_000288.4(PEX7):c.429del (p.Val144fs)PEX7Pathogenic/Likely pathogeniccriteria provided, multiple submitters, no conflicts
639671NM_000288.4(PEX7):c.130+1G>APEX7Pathogeniccriteria provided, multiple submitters, no conflicts
7780NM_000288.4(PEX7):c.875T>A (p.Leu292Ter)PEX7Pathogeniccriteria provided, multiple submitters, no conflicts
7781NM_000288.4(PEX7):c.653C>T (p.Ala218Val)PEX7Pathogenic/Likely pathogeniccriteria provided, multiple submitters, no conflicts
7782NM_000288.4(PEX7):c.649G>A (p.Gly217Arg)PEX7Pathogenic/Likely pathogeniccriteria provided, multiple submitters, no conflicts
7783NM_000288.4(PEX7):c.694C>T (p.Arg232Ter)PEX7Pathogeniccriteria provided, multiple submitters, no conflicts
7785NM_000288.4(PEX7):c.903+1G>CPEX7Pathogeniccriteria provided, multiple submitters, no conflicts
7786NM_000288.4(PEX7):c.345T>G (p.Tyr115Ter)PEX7Pathogeniccriteria provided, multiple submitters, no conflicts
7788NM_000288.4(PEX7):c.120C>G (p.Tyr40Ter)PEX7Pathogeniccriteria provided, multiple submitters, no conflicts
7790NM_000288.4(PEX7):c.40A>C (p.Thr14Pro)PEX7Pathogenic/Likely pathogeniccriteria provided, multiple submitters, no conflicts
813363NM_000288.4(PEX7):c.188+1G>APEX7Pathogenic/Likely pathogeniccriteria provided, multiple submitters, no conflicts

Genes & proteins

Mendelian disease overlap and somatic drivers

GenCC: 0 · Orphanet: 8 · OMIM-shared: 0 · Dual-evidence (GWAS+Mendelian): 0

Orphanet rare-disease linkage (cohort genes)

GeneOrphanet IDRare disease
AGPSOrphanet:309803Rhizomelic chondrodysplasia punctata type 3
GNPATOrphanet:309796Rhizomelic chondrodysplasia punctata type 2
PEX7Orphanet:309789Rhizomelic chondrodysplasia punctata type 1
PEX7Orphanet:773Adult Refsum disease
PEX5Orphanet:44Neonatal adrenoleukodystrophy
PEX5Orphanet:468717Rhizomelic chondrodysplasia punctata type 5
PEX5Orphanet:772Infantile Refsum disease
PEX5Orphanet:912Zellweger syndrome

Cohort genes → proteins

4 cohort genes, 4 distinct canonical proteins.

Evidence partition

SubsetGenes
multi_evidence4

Cohort genes (full)

SymbolHGNCEnsemblUniProtNameEvidence
AGPSHGNC:327ENSG00000018510O00116Alkyldihydroxyacetonephosphate synthase, peroxisomalclinvar
GNPATHGNC:4416ENSG00000116906O15228Dihydroxyacetone phosphate acyltransferaseclinvar
PEX7HGNC:8860ENSG00000112357O00628Peroxisomal targeting signal 2 receptorclinvar
PEX5HGNC:9719ENSG00000139197P50542Peroxisomal targeting signal 1 receptorclinvar

Cohort function summary

Lead sentence per gene, UniProt-curated.

SymbolProtein nameFunction (lead sentence)
AGPSAlkyldihydroxyacetonephosphate synthase, peroxisomalCatalyzes the exchange of the acyl chain in acyl-dihydroxyacetonephosphate (acyl-DHAP) for a long chain fatty alcohol, yielding the first ether linked intermediate, i.e. alkyl-dihydroxyacetonephosphate (alkyl-DHAP), in the pathway of ether…
GNPATDihydroxyacetone phosphate acyltransferaseDihydroxyacetonephosphate acyltransferase catalyzing the first step in the biosynthesis of plasmalogens, a subset of phospholipids that differ from other glycerolipids by having an alkyl chain attached through a vinyl ether linkage at the…
PEX7Peroxisomal targeting signal 2 receptorReceptor required for the peroxisomal import of proteins containing a C-terminal PTS2-type peroxisomal targeting signal.
PEX5Peroxisomal targeting signal 1 receptorReceptor that mediates peroxisomal import of proteins containing a C-terminal PTS1-type tripeptide peroxisomal targeting signal (SKL-type).

Protein-family classification

Druggable: 2 · Difficult: 1 · Unknown: 1 · Druggable fraction: 0.5

Family distribution

Cohort families vs a genome-wide background (hypergeometric, BH-FDR; fold = observed/expected). Counts kept; sorted by enrichment, so the catch-all Other/Unknown bucket no longer leads.

FamilyGenesFoldFDR
Enzyme (other)26.0×0.112
Scaffold/PPI14.3×0.318
Other/Unknown10.5×0.962

Per-gene assignment

SymbolFamilyDruggable?ECInterPro (top 3)
AGPSEnzyme (other)yes2.5.1.26FAD-bd_oxidored_4_C, Oxid_FAD_bind_N, FAD-linked_Oxase-like_C
GNPATEnzyme (other)yes2.3.1.42Plipid/glycerol_acylTrfase, GPAT/DHAPAT, DHAPAT
PEX7Scaffold/PPInoWD40_rpt, WD40/YVTN_repeat-like_dom_sf, WD40_repeat_CS
PEX5Other/UnknownnoTPR-like_helical_dom_sf, TPR_rpt, PEX5/PEX5L

Expression context

Cohort genes with no expression data: 0.

4 cohort genes are a single-cell marker in ≥1 SCXA experiment.

Breadth distribution (Bgee present_calls)

BucketGenes
narrow (1-5 tissues)0
moderate (6-20)0
broad (>20)4
unknown0

Top tissues across cohort

TissueCohort genes
sperm2
calcaneal tendon1
tendon1
biceps brachii1
gluteal muscle1
skeletal muscle tissue of biceps brachii1
esophagus squamous epithelium1
pigmented layer of retina1
gastrocnemius1
left testis1
right testis1

Per-gene tissue summary (top 30)

SymbolBgee breadthFANTOM5 breadthSCXATop tissues
AGPS278ubiquitousmarkersperm, calcaneal tendon, tendon
GNPAT294ubiquitousmarkergluteal muscle, biceps brachii, skeletal muscle tissue of biceps brachii
PEX7276ubiquitousmarkerpigmented layer of retina, sperm, esophagus squamous epithelium
PEX5142ubiquitousmarkergastrocnemius, left testis, right testis

Protein interactions among cohort

Intra-cohort edges: 5.

Hub genes (top 10 by interactor count)

SymbolInteractor count
AGPS2,656
PEX51,741
GNPAT1,641
PEX71,356

Intra-cohort edges

ABSources
AGPSGNPATstring_interaction
AGPSPEX5string_interaction
AGPSPEX7string_interaction
GNPATPEX7string_interaction
PEX5PEX7intact, string_interaction

Structural data

PDB: 1 · AlphaFold-only: 3 · No structure: 0

Cohort genes with PDB structures (top 30)

SymbolUniProtPDB entries
PEX5P5054211

AlphaFold-only cohort genes (top 30 by pLDDT)

SymbolUniProtpLDDT
PEX7O0062895.54
AGPSO0011689.27
GNPATO1522888.96

Function

Pathway analysis

Distinct Reactome pathways touched by cohort: 10. Enrichment computed across 4 evidence-associated genes (4 with Reactome annotation).

Pathways by enrichment

Over-representation of cohort genes vs the genome-wide background (hypergeometric test, Benjamini-Hochberg FDR; fold = observed/expected over 4 annotated cohort genes). Counts and members are kept as ground-truth; sorted by enrichment.

PathwayCohort genesFoldFDRSample cohort genes
Peroxisomal protein import4173.0×1e-08AGPS, GNPAT, PEX7, PEX5
Plasmalogen biosynthesis21903.3×1e-06AGPS, GNPAT
Wax and plasmalogen biosynthesis1951.7×0.004AGPS
TYSND1 cleaves peroxisomal proteins1356.9×0.007AGPS
Pexophagy1237.9×0.008PEX5
Synthesis of PA173.2×0.023GNPAT
E3 ubiquitin ligases ubiquitinate target proteins148.4×0.026PEX5
Protein localization147.6×0.026AGPS
Metabolism of lipids17.9×0.134AGPS
Metabolism12.9×0.302AGPS

GO biological processes by enrichment

Over-representation of cohort genes vs the genome-wide background (hypergeometric test, Benjamini-Hochberg FDR; fold = observed/expected over 4 annotated cohort genes). Counts and members are kept as ground-truth; sorted by enrichment.

GO termCohort genesFoldFDRSample cohort genes
ether lipid biosynthetic process31404.3×1e-08AGPS, GNPAT, PEX7
protein targeting to peroxisome2842.6×3e-05PEX7, PEX5
protein import into peroxisome matrix2702.2×3e-05PEX7, PEX5
fatty acid beta-oxidation2187.2×3e-04PEX7, PEX5
neuron migration266.9×0.002PEX7, PEX5
cerebellum morphogenesis11404.3×0.004GNPAT
protein import into peroxisome matrix, docking11053.2×0.004PEX5
protein import into peroxisome matrix, translocation11053.2×0.004PEX5
protein import into peroxisome matrix, substrate release1842.6×0.004PEX5
paranodal junction assembly1702.2×0.004GNPAT
protein import into peroxisome membrane1702.2×0.004PEX5
mitochondrial membrane organization1601.9×0.004PEX5
protein import into peroxisome matrix, receptor recycling1601.9×0.004PEX5
cerebral cortex cell migration1383.0×0.006PEX5
cerebral cortex neuron differentiation1300.9×0.007PEX5
pexophagy1263.3×0.007PEX5
lipid biosynthetic process1247.8×0.007AGPS
cell development1221.7×0.008PEX5
peroxisome organization1200.6×0.008PEX7
very long-chain fatty acid metabolic process1191.5×0.008PEX5
protein tetramerization1156.0×0.009PEX5
endochondral ossification1135.9×0.009PEX7
neuromuscular process1131.7×0.009PEX5
phosphatidic acid biosynthetic process1127.7×0.009GNPAT
membrane organization1127.7×0.009GNPAT
positive regulation of multicellular organism growth1123.9×0.009PEX5
negative regulation of protein-containing complex assembly1113.9×0.010PEX5
endoplasmic reticulum organization1105.3×0.010PEX5
cellular response to reactive oxygen species1102.8×0.010PEX5
synapse assembly157.7×0.017GNPAT

Therapeutics

Drug target analysis

Approved (phase 4): 0 · Phase ≥3: 0 · Phased (≥1): 0 · Undrugged: 4

Druggability breadth: 2 of 4 evidence-associated genes (50%) have a ChEMBL target (buckets above are over the deeply-mined display cohort).

Top cohort targets by molecule count

SymbolMoleculesMax phase
AGPS00
GNPAT00
PEX700
PEX500

Bioactivity and enzyme data

Enzyme cohort genes (≥1 EC): 2.

Cohort genes with ChEMBL bioactivity (full, sorted by assay count)

SymbolAssaysType breakdown
GNPAT14Functional:8, Binding:6
AGPS5Binding:5

Cohort enzymes (BRENDA EC)

SymbolEC numbersNames
AGPS2.5.1.26alkylglycerone-phosphate synthase
GNPAT2.3.1.42glycerone-phosphate O-acyltransferase

Pharmacogenomics

Cohort genes with a PharmGKB record: 4; with CPIC/DPWG dosing guidelines: 0.

No cohort gene has a CPIC/DPWG genotype-guided dosing guideline (PharmGKB).

Chemical tractability of cohort targets

0 approved/phased compounds have measured bioactivity against a cohort gene (and aren’t yet in disease-level trials). This is a research / tractability signal, NOT a therapeutic recommendation — a bioactivity row often reflects off-target or screening binding (e.g. promiscuous kinase inhibitors against a cohort kinase), implying no disease mechanism.

Druggability pyramid

Cohort genes binned by druggability tier (high → low):

TierDefinitionGenesSymbols
AApproved (phase 4 drug)0
BPhased (≥1) drug, not yet approved0
CDruggable family + PDB, no drug0
DDruggable family + AlphaFold only, no drug2AGPS, GNPAT
EDifficult family or no structure, no drug2PEX7, PEX5

Undrugged target profiles

4 cohort genes are undrugged. Ranked by ‘starting-point quality’ (assay depth + drugged-partner adjacency).

SymbolChEMBL assaysDrugged partners (top 3)
AGPS5
GNPAT14
PEX70
PEX50

Clinical trials & evidence

Clinical trials

Clinical trials: 2.

Phase distribution (across all retrieved trials)

PhaseTrials
PHASE11
Not specified1

Top trials by phase / activity

NCTPhaseStatusTitle
NCT05969977PHASE1UNKNOWNA First-in-Human Phase 1 Study of Plasmalogen Precursor PPI-1011 in Healthy Adult Volunteers to Assess Safety, Tolerability, and Pharmacokinetics
NCT04031287Not specifiedUNKNOWNRCDP Natural History Study

Drugs tested across these trials (top 30)

MoleculeMax phaseTrials referencing
PPI-101111